\Header{plotDistributions}{Visualise Distributions}
\keyword{hplot}{plotDistributions}
\begin{Description}\relax
Boxplot like visualisation of distributions, only the boxes,
i.e. the median and the second and third quartile are plotted
(cf. \code{boxplot.stats} for the details on the calculation).
The plots may help to identify shortcomings of the raw data
or normalised data. The argument \code{quantiles} can be used
to visualize two or three arbitrary quantiles with boxes.
\end{Description}
\begin{Usage}
\begin{verbatim}plotDistributions(dataMatrix, transFunc, quantiles, main, labels, xlab, ylab, colourVector, width=8, height=6, fileName="plotDistributionsOutput", savePath, plotOutput="standard")\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{dataMatrix}] numeric data matrix,
where columns represent distributions, e.g.
raw array data or normalised data;
required; default missing
\item[\code{transFunc}] unary function; optional; default missing.
Data transformation function, e.g. log
\item[\code{quantiles}] missing by default; a vector of two or
three increasing quantiles used to determine the boxes to be drawn
\item[\code{main}] plot title; type character string; optional; default missing
\item[\code{labels}] vector of names, may substitute column names
of \code{dataMatrix}; optional; default missing
\item[\code{xlab}] label for x axis; type character string; optional; default missing
\item[\code{ylab}] label for y axis; type character string; optional; default missing
\item[\code{colourVector}] vector of colours; optional; default missing
\item[\code{width}] graphics window width; required; default: 8
\item[\code{height}] graphics window height; required; default: 6
\item[\code{fileName}] optional; default: "plotDistributionsOutput"
\item[\code{savePath}] optional; default: missing
\item[\code{plotOutput}] character string specifying
either "standard", "screen", "pdf", "win.metafile"; default: "standard"
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Default of \code{transFunc} is no transformation, i.e. identity.
If \code{labels} are supplied at first the column names or
secondly a numbering  are used instead.
By default the \code{colourVector} is defined as alternating
"darkred" and "darkgreen".
\end{Details}
\begin{Value}
The function is called for its side effect.
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{boxplot.stats}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
      plotDistributions(cbind(rnorm(100),rnorm(100)),
             main="Random Gaussians", labels = c("N1","N2"), ylab="scale")
      plotDistributions(as.matrix(1:100), quantiles=c(0.25,0.85),
             main = "Random Gaussians", labels = c("N1"), ylab = "scale")\end{ExampleCode}
\end{Examples}

